Recent reports from the Indian SARS-CoV-2 Genomics Consortium (INSACOG) indicate that a sub-lineage AY.12 of the Delta variant of Covid-19, formerly categorized in Israel, is currently spreading across various regions of India. The INSACOG is an amalgamation of multiple laboratories and agencies across India, responsible for keeping track of genomic variations in the SARS-CoV-2 through a sentinel sequencing effort.
The Role of INSACOG and AY.12 Reclassification
The INSACOG has made claims of numerous cases previously classified as Delta, now being reclassified as AY.12 in India. This reclassification is under intense scrutiny. Primarily aimed at aiding micro-epidemiology, this reclassification is not based on any significant mutation acquisition. It is still unknown whether AY.12 is clinically different from Delta.
No worrying factors have been associated with AY.12 so far. However, it has caught INSACOG’s attention as it reportedly drives the surge in Israel despite a vaccination rate of 60%.
The Delta Variant and its Characteristics
The B.1.617.2, popularly known as the Delta variant, is considered to spread more rapidly than other virus variants. This variant is highly infectious, boasting over twice the contagiousness of previous variants. The Delta variant has further given birth to several sub-lineages, known as ‘Delta plus’ variants, which carry most of its characteristic mutations but differ in other aspects.
Understanding the Higher Infectivity of the Delta Variant
Researchers suggest that a key amino acid mutation might be responsible for the higher infectivity of the Delta variant. They have identified a single mutation that alters an amino acid in the SARS-CoV-2 spike protein, termed as P681R. This mutation transforms a proline residue into arginine, another amino acid. Proline’s presence disrupts the protein’s secondary structure by inhibiting its backbone to conform to alpha-helix or beta-sheet conformation.
Understanding Virus Variants and their Evolution
A virus variant is characterized by one or more mutations that set it apart from other circulating variants. While most mutations are detrimental for the virus, some mutate to help the virus survive. The SARS-CoV-2 virus, which causes COVID-19, is evolving rapidly due to the massive scale at which it has infected individuals globally. High levels of circulation enable the virus to mutate faster as it has higher replication rates.
